March 2014 - galaxy-user - lists.galaxyproject.org

Re: [galaxy-user] File upload
by Jennifer Jackson 12 Mar '14

12 Mar '14

Hi Scott, I am sorry that you have been having problems - and hope that I can help. I just tested FTP right now - and it is working for me. My guess is that the server name being entered is incorrect. You want this to be "usegalaxy.org" (not "use_*r*_galaxy.org") for the main public site (or be whatever the base url is for the other public servers, that are supporting FTP, you may be using). On any server, this is generally noted on the 'Upload File' tool itself, in the FTP section paragraph. This is the section for the public server: The window on this tool is only appropriate for two types of upload functions, either typing in text or entering a remote URL where data is available. This remote URL could be to a FTP server, but the process is different from loading local data (on your own computer) via FTP to the Galaxy server. The video (also linked from the wiki) for this tool demonstrates all four methods for loading data. The first method is a basic browser upload of a small file - which seems to be what you are asking about - how can I help more with this part? http://vimeo.com/galaxyproject/upload For deleting data, you can either delete individual datasets or complete histories. Which are you having trouble with? There are two videos on this wiki about datasets/histories, but it sounds like they are not covering the part you need to know. If you want to provide more details, I can try to help. https://wiki.galaxyproject.org/Learn/Managing%20Datasets The server has been problematic this week, due to circumstances out of our direct control, so if you had problems earlier, trying again is most likely a good first pass solution. You can follow our Twitter feed for updates about Main @galaxyproject - posted on our wiki here: https://wiki.galaxyproject.org/Galaxy%20on%20Twitter Usability matters, so helping you to get these operations working will probably help others as well. And I can add into our documentation what is unclear or missing. Plus most of our wiki is open - community members are encouraged to add new pages or comments to fill in/share help ideas. Thanks! Jen Galaxy team On 3/12/14 2:11 PM, Scott Tighe wrote: > Jennifer > > It is a total mystery how to get data uploaded. Just like it is a > total mystery how to delete it. Spent an hour and a half reviewing > your tutorials and trying FTP. The FTP does not work anymore and if > you put the term usergalaxy.org in to the FTP window, it does not like > that. The tutorials were not useful and appear to be based on FTP. > Maybe you could do a tutorial on how exactly to upload like 10gB. Arrggg > > Thanks > Scott Tighe > Senior Core Laboratory Research Staff > Advanced Genome Technologies Core > NextGen Sequencing/Flow Cytometry > University of Vermont and Vermont Cancer Center > 149 Beaumont ave > Health Science Research Facility 303/305 > Burlington Vermont 05405 > 802-656-2482 (AGTC) > On 3/12/2014 1:17 PM, Jennifer Jackson wrote: >> Hi Scott, >> >> Is the 'Get Data -> Upload File' tool no longer functioning for you? >> Can I help with using Main or is this on a local/cloud instance that >> needs to be set up? >> https://wiki.galaxyproject.org/Support#Loading_data >> >> It is correct that the addition upload methods via the "Load Data" >> process - found at the top of the tool panel - are not included in >> our tutorials/vidoes yet. This is very new set of methods (first was >> placed on Main at the end of January) and may still undergo some >> changes. We expect this to stabilize near-term and then be >> documented. Both tools will continue to co-exist. >> >> If there are any usage question right now (you or others) please let >> us know and we can help. The functions are either the same or very >> similar to the 'Upload File' tool, just presented in a different >> pop-up interface, plus now include convenience/feedback features. >> >> Thanks! >> >> Jen >> Galaxy team >> >> On 3/12/14 12:57 PM, Scott Tighe wrote: >>> For all users: >>> >>> The tutorial on uploading data is incorrect. I do not think they >>> have updated "how to upload data" yet. >>> >>> Scott >>> Scott Tighe >>> Senior Core Laboratory Research Staff >>> Advanced Genome Technologies Core >>> NextGen Sequencing/Flow Cytometry >>> University of Vermont and Vermont Cancer Center >>> 149 Beaumont ave >>> Health Science Research Facility 303/305 >>> Burlington Vermont 05405 >>> 802-656-2482 (AGTC) >> >> -- >> Jennifer Hillman-Jackson >> http://galaxyproject.org > -- Jennifer Hillman-Jackson http://galaxyproject.org

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Enquiry regarding the working of Galaxy
by Sathya 12 Mar '14

12 Mar '14

Now the galaxy main server is not working. I would like to know how long it will take for galaxy to work again. -- With regards, Sathya.B

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Update from server failed several times
by Meike.Latz＠mdc-berlin.de 12 Mar '14

12 Mar '14

Hello, I deleted some files, because I reached 100% of the data volume I could use; my actual volume is 76 GB. I'm waiting now for an update from the server, that I reduced the data volume and can continue with my analysis. But I got a red note on the history for several times, that the update failed and that I should contact you, when it does so. What could I do now, to get an update from the server? Thanks in advance! Best, Meike

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Re: [galaxy-user] can galaxy analyze SOLiD XSQ dataset except csfasta/qual data?
by Chandran, Uma 12 Mar '14

12 Mar '14

Are there mappers for SoLiD 5500 on Galaxy? If so, do they take csfasta files as input? Thanks Uma Chandran

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Cuffdiff output
by Malik, Shivani 12 Mar '14

12 Mar '14

Hi, I have a question about interpreting the cuffdiff data and how to pick up significant genes. I have genes which show ~8 fold change between 2 conditions: eg from FPKM of 0.08 to 28 and yet they are not significant. Is there is threshold of FPKM below which Cuffdiff does not consider it an FPKM to be valid and hence significance in "no"? What downstream analysis should I use to extract a meaningful list of genes from the Cuffdiff data? Also, I filtered out FPKMs which were below 5 in both conditions? Is that reasonable? Thanks Shivani

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Help: Mapping with Bowtie does not start
by Meike.Latz＠mdc-berlin.de 10 Mar '14

10 Mar '14

Hello, I am trying to map sequences with Bowtie for Illumina. I have been waiting for a whole day now but it still says "Job is waiting to run". Are the jobs stuck in a queue or is there any other problem? Thanks a lot in advance! Meike

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Column Join feature
by Justin Clarke 07 Mar '14

07 Mar '14

Hi, I am analysing some RNA-seq data and have two different datasets, total RNA plus enzyme and total RNA minus enzyme. I used to type in "column join" in the "Tools" menu on the Galaxy homepage after uploaded the files in Text delimited format. Column join allowed me to join two datasets by a hinge column, in this case I would choose column 1 which would be the chromosome position. I would also be allowed to fill empty columns with a value of 1. The output would give me 3 columns, chromosome number (which both datasets shared), reads for minus enzyme, and reads for plus enzyme. The function would never reject any chromosome position with reads in one dataset and not the other. However, I cannot seem to be able to find this function anymore, and the new function "Join two datasets" seems to only give me back rows where both plus and minus datasets have reads. Does anyone else have this problem or know how I could get around it? Regards, Justin ---------------------------------- Justin Clarke McDowall Laboratory Garstang 8.52/8.51 Faculty of biological sciences University of Leeds Leeds LS2 9JT

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Galaxy - error
by Flávia Aburjaile 07 Mar '14

07 Mar '14

Dear Malito, I am PhD student and I am working with a bacterial transcriptome. A few days ago, i have a problem to obtain data in DESeq and Edge-r on the plataform galaxy. I get the message "no peek" at the end of the process, even with the task g reen. Have you had this problem? I would like to find a solution... Thank you, -- Flavia Figueira Aburjaile

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Compute an expression
by Hamid Qaedi 07 Mar '14

07 Mar '14

Dear All I have a tabular file and using compute (version 1.1.0) tool under text manipulation menu, I 'm going to do a computation to find rows in which column2 and 3 (c2 and c3) are similar in values (values are A,T,C and G) . It seems the syntax for doing that is "c2==c3", but it dosent work. Can anybody help? Any help would be appreciated. Hamid

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Align many FASTA files
by Jennifer Jackson 05 Mar '14

05 Mar '14

Hi Kristen, Are these longer RNA sequences, such as transcripts? Then a tool like BLAT (or BLAST) would be a good choice. Both are wrapped for Galaxy and available in the Tool Shed for use with a local, cloud, or slipstream Galaxy. A cloud is probably the simplest choice for many users - and if the work is for research purposes, be sure to check out Amazon's grant program. http://usegalaxy.org/cloud http://usegalaxy.org/toolshed The public Main server at http://usegalaxy.org has mappers, but these are tuned for NGS reads. Other public Galaxy servers can offer mapping services, too. There are 50+ to review and what each offers changes over time. If you want to look, here is the list: https://wiki.galaxyproject.org/PublicGalaxyServers Keeping questions on the mailing lists helps us with tracking and is appreciated! https://wiki.galaxyproject.org/MailingLists Thanks, Jen Galaxy team https://wiki.galaxyproject.org/Support https://wiki.galaxyproject.org/BigPicture/Choices On 3/5/14 8:43 AM, Kristin Kernohan wrote: > Hi Jennifer > > I am wondering if there is a way on Galaxy to align to the genome a > file with many (~32000) fasta formatted sequences? > > Thanks very much > > Kristin -- Jennifer Hillman-Jackson http://galaxyproject.org

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